1JBG,1Q05,1EXI


Conserved Protein Domain Family
HTH_MerR-like

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cd00592: HTH_MerR-like 
Click on image for an interactive view with Cn3D
Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators
Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Statistics
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PSSM-Id: 133378
View PSSM: cd00592
Aligned: 124 rows
Threshold Bit Score: 42.2315
Threshold Setting Gi: 29833868
Created: 6-Mar-2002
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
DNA bindingdimer interface
Conserved site includes 7 residues -Click on image for an interactive view with Cn3D
Feature 1:DNA binding residues [nucleic acid binding site]
Evidence:
  • Structure:1EXI; Bacillus subtilis BmrR bound to DNA; defined at 3.5A contacts.
    View structure with Cn3D
  • Comment:these residues contact two consecutive major grooves

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1         ###             #                 ###                                          
1JBG_A         3 YQVKQVAEISGVSIRTLHHYDNIELLnpSALTDa-GYRLYSdADLERLQQILFFKe--IGFRLDEIKEMLDhpnfd---- 75
1EXI_A         6 YSIGEVSKLANVSIKALRYYDKIDLFkpAYVDPdtSYRYYTdSQLIHLDLIKSLKy--IGTPLEEMKKAQDlemee---- 79
gi 106893838   1 MKTMDVCNRLGVTPKGLRVYEEKGLVv-PKRNKn-GYRNYSdIDMLRLREILLLKd--LGFSLQEIKVLLDkniddg--- 73
gi 109646269   1 MQIKEVCEKCKLTKKAIEYYESKNLIh-PQILEn-GYRDYSdADIAVLKEISVLRk--CGVSIADIAEILTssnkpaala 76
gi 15895716    1 MNTKKVCEKLKISPKALRLYEELNIIv-PNRDEn-NYRNYSeDDLFKLRQVVVLKs--IGIKLKSIKDILDkrkyed--- 73
gi 28379183   13 FSTKEVVAITGMTKDALRYYEQQRLIgpVPRNHn-NYRQYSrQNLERLQFVATFRqlgLDLKLLSGDGHIPnraqriqe- 90
gi 28379524   13 FTTKEVTAMTGMTKDALRYYEHLGILpdVQRNQy-NYRQYShKNLETLQLIKIFRdldLDLSLLTPAHLALdgqa----- 86
gi 56965272    1 MQIKDFADKYQMQADTIRYYEKQNLLk-PKRREn-GYREYDeECEKQLQLIVVLKq--LGFTIKEIQQLLIlkgkaisae 76
gi 90573503    1 MTIKEVEEKTGLTRSNIRFYENENLIk-PLRNErnGYREYSdENVEDIKKIAYLRt--LGITIDDIRNIILqkvs----- 72
gi 70725250    1 MQIDEVSKKLNISKSMIRYYEEKGLIn-ISRNQn-NYREFNqTVYTTLKLIKDLKr--LNLSLEEIKYIVNlfnkp---- 72
                         90       100
                 ....*....|....*....|....*..
Feature 1                                   
1JBG_A        76 ----rkaaLQSQKEILMKKKQRMDEMI 98
1EXI_A        80 ----lfafYTEQERQIREKLDFLSALE 102
gi 106893838  74 --yvfvrsLYFQKQAIQKKIQGLKNIE 98
gi 109646269  77 kckyitelRMQRLNDIQKCMDSLIANY 103
gi 15895716   74 --nkvvniLYMQLKAVENRILELKKIE 98
gi 28379183   91 -lssyratVKKQIAQLQATDQFLAHKI 116
gi 28379524   87 ----kvvaFKQYQQVIRDRIRHLEAID 109
gi 56965272   77 cnlsttslLEQKVSDVEEKIQFYQHAL 103
gi 90573503   73 ----lvevVEKQEKVLETKISDLENAK 95
gi 70725250   73 ---tskecNIQSTKYLDRIIKDYKRSI 96

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